After re-estimating my transcripts using stringtiemerge with -eB option, I want to do differential expression analysis at the gene level. For that, I tried Ballgown as well as DESeq2 (after getting raw counts using prepDE3). I got the results but my problem is that I only got gene names or gene ids. Use of either Ballgown or DESeq2 leads to lose of genomic features of the genes such as chr, start, end, strand. It is particularly challenging to find the correct coordinates from the original gtf file since multiple transcripts from a gene may or may not be merged into a single gene. Is there a way to have differential GENE expression while retaining their genomic information?
After re-estimating my transcripts using stringtiemerge with -eB option, I want to do differential expression analysis at the gene level. For that, I tried Ballgown as well as DESeq2 (after getting raw counts using prepDE3). I got the results but my problem is that I only got gene names or gene ids. Use of either Ballgown or DESeq2 leads to lose of genomic features of the genes such as chr, start, end, strand. It is particularly challenging to find the correct coordinates from the original gtf file since multiple transcripts from a gene may or may not be merged into a single gene. Is there a way to have differential GENE expression while retaining their genomic information?
Thanks